Abstract

BACKGROUND. Sphingolipids are important components of cellular membranes and functionally associated with fundamental processes such as cell differentiation, neuronal signaling, and myelin sheath formation. Defects in the synthesis or degradation of sphingolipids leads to various neurological pathologies; however, the entire spectrum of sphingolipid metabolism disorders remains elusive. METHODS. A combined approach of genomics and lipidomics was applied to identify and characterize a human sphingolipid metabolism disorder. RESULTS. By whole-exome sequencing in a patient with a multisystem neurological disorder of both the central and peripheral nervous systems, we identified a homozygous p.Ala280Val variant in DEGS1, which catalyzes the last step in the ceramide synthesis pathway. The blood sphingolipid profile in the patient showed a significant increase in dihydro sphingolipid species that was further recapitulated in patient-derived fibroblasts, in CRISPR/Cas9–derived DEGS1-knockout cells, and by pharmacological inhibition of DEGS1. The enzymatic activity in patient fibroblasts was reduced by 80% compared with wild-type cells, which was in line with a reduced expression of mutant DEGS1 protein. Moreover, an atypical and potentially neurotoxic sphingosine isomer was identified in patient plasma and in cells expressing mutant DEGS1. CONCLUSION. We report DEGS1 dysfunction as the cause of a sphingolipid disorder with hypomyelination and degeneration of both the central and peripheral nervous systems. TRIAL REGISTRATION. Not applicable. FUNDING. Seventh Framework Program of the European Commission, Swiss National Foundation, Rare Disease Initiative Zurich.

Figure 1

Clinical phenotype with progression of spasticity, notably in the arms and hands. Patient at the age of 6 years (A), 13 years (B), 15 years (C), and at last followup at 22 years (D). T2-weighted MRI of the brain, axial (E, and G–I) and sagittal (F and J), at 11 years of age (E and F) and 16 years (G–J). Severe and slowly progressive cerebellar atrophy with fiber degeneration of the middle cerebellar peduncles. The patient shows mild cortical atrophy and thin white matter, especially in the posterior brain regions. In summary, MRI findings are in line with a progressive global neurodegenerative process. (K–N) Electron micrographs of the sural nerve biopsy performed at the age of 2 years reveals nerve fibers with disproportionately thin myelin sheaths (K, arrows). Scale bar: 3 μm. (L) Occasional, moderate myelin folding. Scale bar: 1.8 μm. (M) Small autophagic vacuoles in the cytoplasm of the Schwann cell of a myelinated nerve fiber (white arrows). Black arrows indicate large autophagic vacuoles containing membranous debris in an adjacent cell, which is covered by a basal lamina and may therefore be either a Schwann cell or a macrophage that has invaded a Schwann cell basal lamina sheath. Scale bar: 0.75 μm. (N) Widening of the endoplasmic reticulum (arrow) of a Schwann cell. Scale bar: 0.5 μm. (O) The pedigree of the family shows the segregation of the DEGS1 variant [NM_003676.3:c.839C>T, p.Ala280Val, Chr1(hg19):g.224380047C>T]. Sanger traces of the affected codon are shown in the index patient and his parents. (P) Domain architecture of the human DEGS1 protein. Position of the mutation is indicated in orange. (Q) Species alignment of the amino acid residues in proximity of the DEGS1 mutation. Mutation highlighted in red. FADS, fatty acid desaturase domain.